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arXiv 0901.1820cond-mat.stat-mechcond-mat.soft
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呼吸过程中气泡的合并问题DNA作为一个相反势的恶性Walker问题

Bubble merging in breathing DNA as a vicious walker problem in opposite potentials

Jonas Nyvold Pedersen, Mikael Sonne Hansen, Tomas Novotny, Tobias Ambjornsson, Ralf Metzler

摘要:

我们研究了两个DNA气泡最初位于弱结构域的合并,并在一个设计的双链DNA结构中被一个更稳定的屏障区域分开。在连续Fokker-Planck方法中,气泡合并的特征时间和相应的分布,以及合并位置沿障碍的分布。低于熔化温度,我们发现一个Kramers型的障碍交叉行为,而在高温下,气泡的角落进行漂移扩散聚结。在计算中,我们映射的问题上的两个恶性步行者在相反的潜力的气泡动力学。我们还提出了一个离散的主方程方法的气泡聚结问题。数值计算和随机模拟的主方程显示出良好的一致性的结果从连续的方法。考虑到聚结状态相对于其中仅重新建立屏障区域的一个或几个碱基对的状态是热稳定的,似乎可能的是,这种类型的设置可以用于在单分子荧光实验中对DNA的热力学稳定性数据以及DNA的解压缩和压缩动力学中所涉及的速率常数的定量研究。

英文摘要:

We investigate the coalescence of two DNA-bubbles initially located at weak domains and separated by a more stable barrier region in a designed construct of double-stranded DNA. In a continuum Fokker-Planck approach, the characteristic time for bubble coalescence and the corresponding distribution are derived, as well as the distribution of coalescence positions along the barrier. Below the melting temperature, we find a Kramers-type barrier crossing behavior, while at high temperatures, the bubble corners perform drift-diffusion towards coalescence. In the calculations, we map the bubble dynamics on the problem of two vicious walkers in opposite potentials. We also present a discrete master equation approach to the bubble coalescence problem. Numerical evaluation and stochastic simulation of the master equation show excellent agreement with the results from the continuum approach. Given that the coalesced state is thermodynamically stabilized against a state where only one or a few base pairs of the barrier region are re-established, it appears likely that this type of setup could be useful for the quantitative investigation of thermodynamic DNA stability data as well as the rate constants involved in the unzipping and zipping dynamics of DNA, in single molecule fluorescence experiments.

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